Soil fungi play an important role in biodegradation of industrially polluted soils. In this study, we isolated the native fungal strains in industrial and city soils, assessed their diversity, and compared them with other fungal strains available in NCBI. Molecular identification of isolated strains had been performed by using 18S rRNA genes. Six strains, Aspergillus flavus, A. niger, Talaromyces funiculosus, A. sublatus, A. nidulans, and A. ustus- were identified by molecular techniques, and phylogenetican alysisshowed their divergent nature as they did not have any close relation to the other worldwide isolates. Possible reason of the genetic diversity lies in the impact of hot climatic conditions prevailing in Saudi Arabia. The concentration of total polycyclic aromatic hydrocarbons (PAHs) and heavy metals was determined to correlate the environment with other biodegradable strains. The native strains of soil fungi mainly depend on the exposure time and organic matter content. It was noted that areas with more plants showed the presence of more and effective fungal strains, and recorded low PAHs. This study, therefore, focused on the use of native strains and their potential for remediation of soils and the homogeneity of fungal strains, which are mainly evident of low organic matter and high salinity in the area. These results lay a strong foundation for providing comprehensive information about bioremediation of PAH-contaminated soils in the future.